1. Chapter 1
Structure and Bonding

2. Chapter 1 - Definitions
Organic Chemistry – is the study of carbon containing compounds.
Orbitals – are the specific regions of an atom which maintains electrons. This is defined by quantum mechanics.
Covalent Bond – is formed when an electron pair is shared between atoms.
Valance Bond Theory – maintains that bonding occurs by the overlapping of two atomic orbitals.

3. Chapter 1 - Definitions
Molecular Orbital (MO) Theory – maintains that bonds results from the mathematical combination of atomic orbitals to give molecular orbitals, which belong to the entire molecule.
Sigma (s) bonds – are bonds that are created by the overlap of two s orbitals (sphere).

4. What is Organic Chemistry?
Organic Chemistry is defined as the study of carbon compounds.
There are 10 atoms which are considered in organic chemistry. These atoms are carbon, nitrogen, oxygen, fluorine, silicon, phosphorous, sulfur, chlorine, bromine, iodine.

5. Defined Organic Molecules1 H 2 He 5 B 6 C 7 N 8 O 9 F 10 Ne 3 Li 4 Be 15 P 11 Na 12 Mg 13 Al 14 Si 16 S 17 Cl 18 Ar 19 K 20 Ca 21 Sc 22 Ti 23 V 24 Cr 25 Mn 26 Fe 27 Co 28 Ni 29 Cu 30 Zn 31 Ga 32 Ge 33 As 34 Se 35 Br 36 Kr 37 Rb 38 Sr 39 Y 40 Zr 41 Nb 42 Mo 43 Tc 44 Ru 45 Rh 46 Pd 47 Ag 48 Cd 49 In 50 Sn 51 Sb 52 Te 53 I 54 Xe 55 Cs 56 Ba 57 La 72 Hf 73 Ta 74 W 75 Re 76 Os 77 Ir 78 Pt 79 Au 80 Hg 81 Tl 82 Pb 83 Bi 84 Po 85 At 86 Rn 87 Fr 88 Ra 89 Ac
104 Rf
105 Db
106 Sg
107 Bh
108 Hs
109 Mt
110 Ds

6. What is Carbon so special?
Carbon has the unique ability to bond together to form long chains or ring structures.
This allows carbon to make tens of billions of molecules.
These molecules can range from DNA and plastics to pharmaceuticals.

7. Review (1) - Nucleus
An atom maintains 2 parts, the nucleus and the shells.
Protons, positively charge particles, and Neutrons, neutral charge particles are found in the nucleus of atoms.
Although small the nucleus maintains all the mass of an atom with both protons and neutrons contributing to the atomic mass.
Rule: All protons and neutrons are found in the nucleus.

8. Review (2) – Electrons and Orbitals
Electrons, negatively charge particles, circle around and through the nucleus in specific orbitals, which defines the electrons path, and shells, which defines the distance from the nucleus. Electron are extremely small when compared to the nucleus and contribute nothing to the molecular mass to the atom.
Orbitals, are probability clouds which determine where the electron might be. This was determined by a mathematical equation called a wave equation, y.

9. 1s Orbital

10. 1s and 2s Orbitals

11. Valance Shell
The Valance Shell is the outermost shell which contains at least one electron.
In this example the 2s is the valance shell.

12. Energy Levels

13. Additional Definitions
Atomic Number (Z) – the number of protons in the atom’s nucleus.
Mass Number (A) – the total number of protons and neutrons in its nucleus.
Atomic Mass – are the weighted average mass unit (amu) of an element’s natural occurring isotopes is called the atomic mass (or atomic weight).

14. Review (3) – Types of Orbitals
There are many orbitals, each with specific number of electrons, distance from the nucleus, and shape.
Specifically there are 4 different types of orbitals, s, p, d, f with organic chemistry focusing on the s and p orbitals.

15. 1s Orbital

16. p Orbitals

17. p Orbitals

18. Three Overlapping p Orbitals

19. 2s + 2p Orbitals

20. 2s + 2p Orbitals

21. Review (4) - Isotopes
Isotopes – atoms with the same atomic number but different mass numbers.
This is done by the addition of neutrons to the nucleus of an atom.
Remember that the mass is from neutrons and protons not electrons.

22. Review (5) – Shell/Orbital Differences
Difference between a shell and a orbital.
An orbital is the specific path that a pair of electron makes around the nucleus.
The shell defines either one or several orbital that are a specific distance away with a node between them.

23. Defined Organic Molecules1 H 2 He 5 B 6 C 7 N 8 O 9 F
10 Ne 3 Li 4 Be 15 P 11 Na 12 Mg 13 Al 14 Si 16 S 17 Cl 18 Ar 19 K 20 Ca 21 Sc 22 Ti 23 V 24 Cr 25 Mn 27 Co 29 Cu 30 Zn 31 Ga 32 Ge 33 As 34 Se 28 Ni 35 Br 26 Fe 36 Kr 37 Rb 38 Sr 39 Y 40 Zr 41 Nb 42 Mo 43 Tc 44 Ru 45 Rh 46 Pd 47 Ag 48 Cd 49 In 50 Sn 51 Sb 52 Te 53 I 54 Xe 55 Cs 56 Ba 57 La 72 Hf 73 Ta 74 W 75 Re 76 Os 77 Ir 78 Pt 79 Au 80 Hg 81 Tl 82 Pb 83 Bi 84 Po 85 At 86 Rn 87 Fr 88 Ra 89 Ac
104 Rf
105 Db
106 Sg
107 Bh
108 Hs
109 Mt
110 Ds
= Orbital (2p)
= Shells (1, 2, 3, 4, 5, 6)

24. Review (6) - Atomic Structure
These numbers denote a series of orbitals that are a certain distance away from the nucleus, that are separated by a node.
A node is a region where electron density is zero, or a space between different shells.

25. Electronic Shells

26. 1 S Electronic Shells

27. 2s + 2p Orbitals

28. Take Home Message General Understanding: 1) Atomic Structure
2) Valance Shell
3) Orbitals vs Shells

29. What are Bonds?
Bond are the either the donation of an electron (ionic) or the sharing of electron(s) (covalent) between two different atoms.

30. Bonding
2 Single Hydrogen Atoms
1 Covalent Bond (H2)

31. Bonding

32. Energy

33. Number of Single Bonds in Organic Chemistry

34. Bonds Formed 1 3 4 3 2 1 2 = Orbital (2p) = Shells (1, 2, 3, 4, 5, 6)1 H 2 He 3 4 3 2 1 2 5 B 6 C 7 N 8 O 9 F
10 Ne 3 Li 4 Be 15 P 11 Na 12 Mg 13 Al 14 Si 16 S 17 Cl 18 Ar 19 K 20 Ca 21 Sc 22 Ti 23 V 24 Cr 25 Mn 26 Fe 27 Co 29 Cu 30 Zn 31 Ga 32 Ge 33 As 34 Se 28 Ni 35 Br 36 Kr 37 Rb 38 Sr 39 Y 40 Zr 41 Nb 42 Mo 43 Tc 44 Ru 45 Rh 46 Pd 47 Ag 48 Cd 49 In 50 Sn 51 Sb 52 Te 53 I 54 Xe 55 Cs 56 Ba 57 La 72 Hf 73 Ta 74 W 75 Re 76 Os 77 Ir 78 Pt 79 Au 80 Hg 81 Tl 82 Pb 83 Bi 84 Po 85 At 86 Rn 87 Fr 88 Ra 89 Ac
104 Rf
105 Db
106 Sg
107 Bh
108 Hs
109 Mt
110 Ds
= Orbital (2p)
= Shells (1, 2, 3, 4, 5, 6)

35. The Octet Rule
The Octet rules states that most organic atoms needs 8 electrons to fill its outer shell. Only one example is found that wants only 2 electrons (HYDROGEN).
Atoms that need 8 electrons: Carbon (C), Nitrogen (N), Oxygen (O), Fluorine (F), Chlorine (Cl), Bromine (Br), Iodine (I).

36. Cheat Sheet (To fufill the octet) This number of bonds are formed:
4 = Carbon (C)
3 = Nitrogen (N), Phosphorus (P)
2 = Oxygen (O), Sulfur (S)
1 = Fluorine (F), Chlorine (Cl), Bromine (Br), Iodine (I),
and Hydrogen (H)

37. Example If you have 1 carbon how many chlorines do you need?
1 carbon makes 4 bonds. Chlorine makes one bond. So you need 1 carbon and 4 chlorines.
CCl4
GeCl4
AlH3
CH2Cl2
CH3NH2
CH4

38. Hint – (chapter 1 only) 1) Look for the Central Atom
The central atoms in organic chemistry is normally Carbon (C), Nitrogen (N), Sulfur (S), and Oxygen (O)
2) Once you have the central atoms in the molecule then they are filled in with Fluorine (F), Chlorine (Cl), Bromine (Br), Iodine (I), and Hydrogen (H)

39. Electron-Dot Structure Examples
1) Find the Central Atom.
2) Place the electrons around it. Make sure that you fill the electrons 1 for each orbital first (4 orbitals) until all electrons around the are used.
3) Then add the electrons from the remaining atoms.
Methane
Ethanol

40. Line Structures Examples
1) Find the Central Atom.
2) Place 1 straight line for each pair of electrons to the remaining atoms.
Methane
Ethanol

41. Line and Electron-Dot Structures
Methane
Ethanol

42. sp3 Orbitals of Carbon (C)
sp3 orbital is the combination the s and p orbitals.
Geometry = oC

43. sp3 Orbitals of Carbon (C)
Normally you have 1s orbital and 3p orbitals. However in the case of Carbon (C) the S and P orbitals merge to form the sp3 orbitals.

44. sp3 Orbitals of Carbon (C)
sp3 orbital is the combination the s and p orbitals.
Example: 4 electrons from Carbon (C) and 4 electrons from the 4 Hydrogens (H)

45. sp2 Orbitals of Carbon (C)

46. sp2 Orbitals of Carbon (C)
sp2 orbitals is the combination of 3 sp orbitals and 1 p orbital. 1 double bond is formed.
Geometry = 120 oC flat.

47. sp2 Orbitals of Carbon (C)

48. sp Orbitals of Carbon (C)

49. sp Orbitals of Carbon (C)
Sp orbitals is the combination of 2 sp orbitals and 2 p orbital. 1 triple bond is formed.
Geometry = 180 oC

50. Structure of Nitrogen, Oxygen, Phosphorus, and Sulfur

51. Molecular Orbital Theory
Combination of atomic orbitals from different atoms to form molecular orbitals.
All of the electrons from each atom is place on an energy diagram which includes both a bonding and anti-bonding level.
Bonding is the lower level.
Anti-bonding is the higher level.
When the Anti-bonding level is totally filled then the bonds are broken and the octet is filled.

52. Molecular Orbital Theory
Bonding is found between two hydrogen atoms
There is no bonding between two helium atoms

53. More Complex Molecular Orbital Diagrams
Bonding is found between two carbon atoms

54. Drawing Skelton Structures
For each carbon bond draw a line that represents one carbon bound to another.
Write out all other atoms except hydrogens bound to the carbon atom. hydrogens fill in the rest of the molecules.
Double and triple bonds are represented by two and three lines respectively.

55. Skelton or Condensed Structures
Name
Skeleton
Total
Isoprene, C5H8
Phenol, C6H6O
Methylcyclohexane, C7H14
Vinyl-benzene, C8H8
Butane, C4H10

56. What is the Skeleton Structure?

57. Things to Know Orbitals Number and Type of Bonding Valance Shell
Octet Rule
sp3, sp2, sp orbital bonding
Electron-Dot, Line, Condensed (Skeleton) Structures